Parasitemia/ParasitemiaUI/Program.fs

   1 module ParasitemiaUI.Main
   2
   3 open System
   4 open System.IO
   5 open System.Threading
   6
   7 open Emgu.CV
   8 open Emgu.CV.Structure
   9
  10 open Logger
  11
  12 open ParasitemiaCore.Utils
  13 open ParasitemiaCore.Config
  14
  15 type Input =
  16     | File of string
  17     | Dir of string
  18
  19 type RunningMode =
  20     | CmdLine of Input * string // A file or a directory to process and the output directory.
  21     | Window of string option // An optional path to a file to open can be given in window mode.
  22
  23 type Arguments = RunningMode * bool
  24
  25 let parseArgs (args : string[]) : Arguments =
  26
  27     let output = Array.tryFindIndex ((=) "--output") args
  28
  29     let runningMode =
  30         match Array.tryFindIndex ((=) "--folder") args, output with
  31         | Some i, Some i_output when i < args.Length - 2 && i_output < args.Length - 2 ->
  32             CmdLine ((Dir args.[i + 1]), args.[i_output + 1])
  33         | _ ->
  34             match Array.tryFindIndex ((=) "--file") args, output with
  35             | Some i, Some i_output when i < args.Length - 2 && i_output < args.Length - 2 ->
  36                 CmdLine ((File args.[i + 1]), args.[i_output + 1])
  37             |_ ->
  38                 Window (if args.Length > 0 && not (args.[0].StartsWith("--")) then Some args.[0] else None)
  39
  40     runningMode, Array.exists ((=) "--debug") args
  41
  42 let showArgsHelp () =
  43     printfn "Usage of Parasitemia :"
  44     printfn "Non-interactive mode:"
  45     printfn "  %s (--folder <folder>|--file <file>) --output <folder> [--debug]" System.AppDomain.CurrentDomain.FriendlyName
  46     printfn "    --folder <folder> : an input folder containing images to analyze"
  47     printfn "    --file <file> : an image file to be analyzed"
  48     printfn "    --output <folder> : a folder to put the results"
  49     printfn "    --debug : output more information like intermediate images if set"
  50
  51     printfn "Interactive mode:"
  52     printfn "  %s [<document-file>] [--debug]" System.AppDomain.CurrentDomain.FriendlyName
  53     printfn "    <document-file> : a PIAZ file to automatically open at startup"
  54     printfn "    --debug : output information like intermediate images if set in the current directory"
  55
  56 [<System.Runtime.InteropServices.DllImport("kernel32.dll")>]
  57 extern bool AttachConsole(int dwProcessId)
  58
  59 [<EntryPoint>]
  60 [<STAThread()>]
  61 let main args =
  62     // To redirect stdout to the attached console.
  63     AttachConsole(-1) |> ignore // -1 to attach to the parent process.
  64
  65     if Array.exists (fun e -> e = "--help" || e = "-h") args then
  66         showArgsHelp ()
  67         0
  68     else
  69         try
  70             Log.User("Starting of Parasitemia UI ...")
  71
  72             let result =
  73                 match parseArgs args with
  74                 | mode, debug ->
  75                     let config = Config(defaultParameters)
  76
  77                     match mode with
  78                     | CmdLine (input, output) ->
  79                         if debug then
  80                             config.Debug <- DebugOn output
  81
  82                         Directory.CreateDirectory output |> ignore
  83
  84                         use logFile = new StreamWriter(new FileStream(Path.Combine(output, "log.txt"), FileMode.Append, FileAccess.Write))
  85                         let listener = { new IListener with member this.NewEntry severity mess = logFile.WriteLine(mess) }
  86                         Log.AddListener(listener)
  87
  88                         Log.User (sprintf "=== New run : %O %s ===" DateTime.Now  (if debug then "[DEBUG]" else "[RELEASE]"))
  89
  90                         let files = match input with
  91                                     | File file -> [ file ]
  92                                     | Dir dir -> Directory.EnumerateFiles dir |> List.ofSeq
  93
  94                         use resultFile = new StreamWriter(new FileStream(Path.Combine(output, "results.txt"), FileMode.Append, FileAccess.Write))
  95
  96                         let images = [ for file in files -> Path.GetFileNameWithoutExtension(FileInfo(file).Name), config.Copy(), new Image<Bgr, byte>(file) ]
  97
  98                         Log.LogWithTime("Whole analyze", Severity.USER, (fun () ->
  99                             match ParasitemiaCore.Analysis.doMultipleAnalysis images None with
 100                             | Some results ->
 101                                 for id, cells in results do
 102                                     let config, img = images |> List.pick (fun (id', config', img') -> if id' = id then Some (config', img') else None)
 103                                     img.Dispose()
 104                                     let total, infected = countCells cells
 105                                     fprintf resultFile "File: %s %d %d %.2f (diameter: %O)\n" id total infected (100. * (float infected) / (float total)) config.RBCRadius
 106                             | None ->
 107                                 fprintf resultFile "Analysis aborted"
 108                             Some ())) |> ignore
 109
 110                         Log.RmListener(listener)
 111                         0
 112
 113                     | Window fileToOpen ->
 114                         if debug then config.Debug <- DebugOn "."
 115                         GUI.run config fileToOpen
 116
 117             Log.User("Parasitemia UI closed")
 118             result
 119
 120         with
 121         | ex ->
 122             Log.Fatal("Error: {0}", ex)
 123             1